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comparison deeparg_predict.xml @ 0:3953324f6d31 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deeparg commit 0f935507a23e554a7d9e181a278a00440865c3ba
author iuc
date Fri, 14 Feb 2025 11:09:55 +0000
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1 <tool id="deeparg_predict" name="DeepARG predict" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <description>Antibiotic Resistance Genes (ARGs) from metagenomes</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="xrefs"/>
7 <expand macro="requirements"/>
8 <command detect_errors="exit_code"><![CDATA[
9 ##Used only for test
10 #if str($hide_db_build) == 'true':
11 deeparg download_data -o '$deeparg_db.fields.path' &&
12 #end if
13 ##
14 mkdir -p deeparg_predict_output &&
15 deeparg predict
16 --model '$model'
17 -i '$input'
18 -o 'deeparg_predict_output/deeparg_predict'
19 -d '$deeparg_db.fields.path'
20 --type '$type'
21 --min-prob $min_prob
22 --arg-alignment-identity $arg_alignment_identity
23 --arg-alignment-evalue $arg_alignment_evalue
24 --arg-alignment-overlap $arg_alignment_overlap
25 --arg-num-alignments-per-entry $arg_num_alignments_per_entry
26 ]]></command>
27 <inputs>
28 <!-- used only for tests, as the deeparg database contains large files that cannot be deleted or reduced. -->
29 <param name="hide_db_build" type="hidden" value=""/>
30 <!-- -->
31 <param name="input" type="data" format="fasta" label="Input file"/>
32 <param name="deeparg_db" type="select" label="DeepARG database">
33 <options from_data_table="deeparg">
34 <filter type="static_value" value="@TOOL_VERSION@" column="db_version"/>
35 <validator message="No deeparg database is available" type="no_options"/>
36 </options>
37 </param>
38 <param argument="--model" type="select" label="Select model to use">
39 <option value="SS" selected="true">SS (short sequences for reads)</option>
40 <option value="LS">LS (long sequences for genes)</option>
41 </param>
42 <param argument="--type" type="select" label="Molecular data type">
43 <option value="nucl" selected="true">Nucleotid (default)</option>
44 <option value="prot">Protein</option>
45 </param>
46 <param argument="--min-prob" type="float" min="0" max="1" value="0.8" label="Minimum probability cutoff [Default: 0.8]"/>
47 <param argument="--arg-alignment-identity" type="integer" min="0" value="50" label="Identity cutoff for sequence alignment [Default: 50]"/>
48 <param argument="--arg-alignment-evalue" type="float" min="0" value="1e-10" label="Evalue cutoff [Default: 1e-10]"/>
49 <param argument="--arg-alignment-overlap" type="float" min="0" max="1" value="0.8" label="Alignment read overlap [Default: 0.8]"/>
50 <param argument="--arg-num-alignments-per-entry" type="integer" min="0" value="1000" label="Diamond, minimum number of alignments per entry [Default: 1000]"/>
51 <section name="output_files" title="Selection of the output files">
52 <param name="output_selection" type="select" label="Output files selection" display="checkboxes" multiple="true">
53 <option value="file_ARG_tsv" selected="true">ARG detected with prob higher or equal to --prob in TSV</option>
54 <option value="file_potential_ARG_tsv" selected="true">ARG detected with prob below --prob in TSV</option>
55 <option value="file_all_hits_tsv" selected="false">All hits detected in TSV</option>
56 </param>
57 </section>
58 </inputs>
59 <outputs>
60 <data name="output_mapping_ARG" format="tabular" from_work_dir="deeparg_predict_output/deeparg_predict.mapping.ARG" label="${tool.name} on ${on_string} : ARG detected (prob higher or equal to --prob)">
61 <filter>output_files['output_selection'] and "file_ARG_tsv" in output_files['output_selection']</filter>
62 </data>
63 <data name="output_mapping_potential_ARG" format="tabular" from_work_dir="deeparg_predict_output/deeparg_predict.mapping.potential.ARG" label="${tool.name} on ${on_string} : Potential ARG (prob below --prob)">
64 <filter>output_files['output_selection'] and "file_potential_ARG_tsv" in output_files['output_selection']</filter>
65 </data>
66 <data name="output_all_hits" format="tabular" from_work_dir="deeparg_predict_output/deeparg_predict.align.daa.tsv" label="${tool.name} on ${on_string} : all hits detected">
67 <filter>output_files['output_selection'] and "file_all_hits_tsv" in output_files['output_selection']</filter>
68 </data>
69 </outputs>
70 <tests>
71 <!-- Test 1 -->
72 <test expect_num_outputs="3">
73 <param name="hide_db_build" value="true"/>
74 <param name="input" value="ORFs.fa" ftype="fasta"/>
75 <param name="deeparg_db" value="deeparg_1.0.4-19122024"/>
76 <param name="model" value="SS"/>
77 <param name="type" value="nucl"/>
78 <section name="output_files">
79 <param name="output_selection" value="file_ARG_tsv,file_potential_ARG_tsv,file_all_hits_tsv"/>
80 </section>
81 <output name="output_mapping_ARG" ftype="tabular">
82 <assert_contents>
83 <has_text text="YP_003283625.1|FEATURES|tet(K)|tetracycline|tet(K)"/>
84 <has_text text="RPOB2"/>
85 </assert_contents>
86 </output>
87 <output name="output_mapping_potential_ARG" ftype="tabular">
88 <assert_contents>
89 <has_text text="gi:545254650:ref:WP_021551023.1:|FEATURES|mdtB|multidrug|mdtB"/>
90 <has_text text="MUXB"/>
91 </assert_contents>
92 </output>
93 <output name="output_all_hits" ftype="tabular">
94 <assert_contents>
95 <has_size value="226000" delta="10000"/>
96 <has_text text="ADV91011.1|FEATURES|RbpA|rifamycin|RbpA"/>
97 </assert_contents>
98 </output>
99 </test>
100 </tests>
101 <help>
102 DeepARG Predict is a computational tool designed to classify and annotate antibiotic resistance genes (ARGs) from nucleotide or protein sequences
103
104 It takes as input a **fasta nucleotide or protein file** containing short (SS model) or long (LS model) sequences
105
106 DeepARG output
107 ---------------
108
109 DeepARG generates two main files: .ARG that contains the sequences with a probability sup or = --prob (0.8 default) and .potential.ARG with sequences containing a probability inf to --prob (0.8 default). The .potential.ARG file can still contain ARG-like sequences, howevere, it is necessary inspect its sequences
110
111 The output format for both files consists of the following fields:
112
113 * ARG_NAME
114 * QUERY_START
115 * QUERY_END
116 * QUERY_ID
117 * PREDICTED_ARG_CLASS
118 * BEST_HIT_FROM_DATABASE
119 * PREDICTION_PROBABILITY
120 * ALIGNMENT_BESTHIT_IDENTITY (%)
121 * ALIGNMENT_BESTHIT_LENGTH
122 * ALIGNMENT_BESTHIT_BITSCORE
123 * ALIGNMENT_BESTHIT_EVALUE
124 * COUNTS
125
126 If you want to annotate paired-end short read sequencing data use the DeepARG Short Reads tool
127
128 </help>
129 <expand macro="citations"/>
130 </tool>